GeneFox

Vindhya Data Science

About this app

GeneFox is a genomics browser for exploring public gene-expression and survival data — from The Cancer Genome Atlas (TCGA), NCBI's Gene Expression Omnibus (GEO), GTEx, UCSC Xena, and the Cancer Cell Line Encyclopedia — right on your device. Statistics and visualizations are computed locally; the app fetches only the public datasets you ask for.

Built for researchers, students, and clinicians who need fast, reproducible look-ups of cancer-genomics data on a phone, tablet, or desktop.

WHAT YOU CAN DO

• Browse 100+ cohorts from the NCI Genomic Data Commons — TCGA, TARGET, CPTAC, CGCI, CMI, APOLLO, and more — with case counts, primary sites, disease types, and an at-a-glance demographics summary.
• Visualize gene-expression distributions across any cohort as box, bar, strip, or violin plots — stratified by clinical variables, molecular subtype, sample type, or the mutation status of any second gene.
• Generate Kaplan–Meier survival curves stratified by clinical variables, gene expression, or mutation status, with log-rank p-values and median survival.
• Compare tumor expression against adjacent-normal and matched GTEx normal tissue via the UCSC Xena TOIL hub, with effect sizes and Mann–Whitney U statistics.
• Chart differential expression as an interactive volcano plot — expression contrasts or mutant-vs-wild-type — with pre-ranked GSEA against bundled Hallmark, KEGG, immune, oncogenic, and cancer-subtype signatures.
• Render gene-panel heatmaps with hierarchical clustering, multi-track annotation strips, Z-normalization, and an outlier-resistant diverging color scale.
• Score any cohort against a custom gene signature, with a distribution histogram, summary statistics, and signature-split survival.
• Test a gene's prognostic value across every TCGA cohort at once with the Pan-Cancer Survival forest plot, then drill into any cohort's curve.
• Search NCBI GEO with smart cancer-term expansion, plus Featured and Recently Viewed discovery tiers.
• Capture any chart into a Report Builder and export a multi-figure PDF or HTML report with an auto-generated methods section.

ASK GENEFOX

Ask questions in plain language — "show TP53 by stage", "correlate BRCA1 and BRCA2", "summarize this cohort" — and get answers as inline, interactive result cards. Questions are interpreted on your device where supported; for harder questions, a privacy-preserving cloud option that you explicitly opt into can help. Either way, your datasets and results stay yours.

PRIVACY

GeneFox has no ads, no analytics, and no third-party tracking, and it doesn't require an account. Bookmarks stay private to you — synced across your devices where your platform supports it, and portable everywhere via export and import. Our Privacy Policy spells out what each feature sends and to whom.

DATA SOURCES

GeneFox displays data from public research repositories. Consult each provider's official site for the authoritative source:
• NCI Genomic Data Commons (TCGA and related programs): https://gdc.cancer.gov
• NCBI Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/
• GTEx Portal: https://gtexportal.org
• UCSC Xena: https://xenabrowser.net
• Cancer Cell Line Encyclopedia (CCLE): https://sites.broadinstitute.org/ccle/

DISCLAIMER

GeneFox is an independent app for scientific and educational use only. It is NOT a government application: it does not represent, and is not affiliated with or endorsed by, any government entity or agency (including the U.S. National Institutes of Health, National Cancer Institute, or NCBI) or any of the data providers above. It does not provide medical advice, diagnosis, or treatment, and its data have not been independently validated for clinical decision-making.

GeneFox is developed by Vindhya Data Science.

What’s new

• Sample PCA — a new plot for GEO and TCGA cohorts: project all samples across all genes and color by clinical or dataset metadata to reveal structure, batch effects, and outliers.
• GEO search now returns dataset Series only (no sample or platform noise).
• Loads larger expression matrices, with a real download progress bar.
• Redesigned GEO filters into a clearer, touch-friendly panel.
• Faster, smoother performance on lower-end devices.